Gendun Gyatso (dge 'dun rgya mtsho) was born in 1476 in the Tanak area of Tsang. He was born to a family of yogic practitioners who had forged a connection to his predecessor the first Dalai Lama, and also had a strong historic connection with Samye Monastery, where an anscestor was an abbot. His paternal grandfather, a Shangpa Kagyu lama named Lama Donyo Gyeltsen, was a disciple of the Sakya patriarch Namkha Neljor (nam mkha' rnal 'byor, 1388-1469/70) and founder of the Sakya monastery Tanak (rta nag). Donyo Gyeltsen’s son, Kunga Gyeltsen (kun dga’ rgyal mtshan, 1432-1481), a disciple of Gendun Drub, was Gendun Gyatso’s father. His mother was Kunga Pelmo (kun dga' dpal mo, d.u.), considered to be a reincarnation of the consort to the Kagyu master Gotsangpa (rgo tsang pa, d.u.). Gendun Drub was born when his father was forty-five years old. He wrote in his autobiography that at the moment of his birth he faced the direction of Tashilhunpo (bkra shis lhun po) and smiled. His birth name was Sangge Pel (sangs rgyas 'phel).

Gendun Gyatso was, by all accounts, an extraordinary child, speaking in song of his previous lives and expressing the wish to return to his monastery, Tashilhunpo to all those who would listen. He records that at three, upon being scolded by his mother, he responded with "Don’t get annoyed at me or I won’t stay, I’ll go back to Tashilhunpo." Soon after a delegation from Tashilhunpo came to his home, and it is said that the child manifested extreme delight at their appearance, greeting each of them by name, and relating to them as if they were old friends.

At this time, in the early years of the Geluk lineage in Tibet, the tradition of recognizing reincarnated lamas was extremely unusual, and Gendun Gyatso remained at home for some time, before being enthroned as the reincarnation of Gendun Drub at Tashilhunpo in 1487. He did, however, receive novice vows at age ten or eleven, when he received the name Gendun Gyatso.

Gendun Gyatso trained at nearby monasteries of Nenying (gnas rnying) Nartang (snar thang), and his family’s monastery of Tanak. It is likely that among the obstacles to his recognition was the reputation of his family, who openly embraced so many different religious traditions. Gendun Gyato’s continued embrace of his family’s eclectic traditions no doubt served him well as he sought to spread Tsongkhapa’s Geluk teachings. This was important because during his youth the Kagyu leaders of Tsang and the Geluk heirarchs of Lhasa were at war, with the Tsangpa occupying Lhasa from 1498 to 1517.

Even before his studies were completed Gendun Gyatso began to teach and give initiations, and was greeted by the faithful in droves. Despite his fame, or, some say, perhaps because of it, Gendun Gyatso found the environment at Tashilhunpo increasingly uncomfortable, and in 1494 left for U, where he studied with Jamyang Lekpai Chojor ('jam dbyang legs pa'i chos 'byor, d.u.) at Drepung Loseling Monastery ('bras spungs blo gsal gling), taking full ordination and completing his studies.

For the next twenty years, Gendun Gyatso spent his life doing practice, pilgrimage, and giving teachings, and developed an enormous following in Tibet. During this time he met and took teachings and instruction from the solitary yogi Khedrub Norsang Gyatso (mkhas grub nor sang rgya mtsho, d.u.), and the two spent many months together practicing and meditating. Gendun Gyatso’s biographies state that he attained enlightenment under the tutelage of this master.

Among the many accomplishments of his life, Gendun Gyatso is remembered for the construction of Chokhor Gyel Metok Tang (chos 'khor rgyal me tog thang) in 1509. Chokkhor Gyel came to be known as the personal monastery of the Dalai Lamas. Gendun Gyatso also was crucial in the empowerment of Lhamo Lhatso (lha mo lha mtsho). This lake continued to play an important role in the recognition of later Dalai Lamas, and is still considered the most powerful source of divinations in Tibet. Gendun Gyatso served as abbot of Tashilhunpo in 1512, and of Drepung in 1517, following the return of Lhasa to Geluk control. In 1528 he became the abbot of Sera. Gendun Gyatso also founded Ngari Dratsang (mnga' ris grwa tshang) in 1541, in response to the growing support for Geluk teachings of the kings of Guge (gu ge) in Ngari. His influence stretched from Ngari to Kham.

Around the year 1530 Gendun Gyatso built the Ganden Podrang (dga' ldan pho brang) at Drepung. It was built on land donated in 1518 by the Pakmodru leader of the time. This came to be the residence of the Dalai Lamas until the Potala was built in the seventeenth century, and gave its name to the government of the Dalai Lamas after the time of the Fifth Dalai Lama.

Gendun Gyatso passed away in 1542. He left behind many volumes of verse, composition, and practice instructions.